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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2020-04-14, 01:44 based on data in: /athena/angsd/scratch/tak76/finalProject


        General Statistics

        Showing 400/400 rows and 8/9 columns.
        Sample Name% AssignedM Assigned% AlignedM Aligned% Dups% GCLengthM Seqs
        Acute_Fatal_1
        45.4%
        3.9
        13.2%
        4.2
        Acute_Fatal_1._STARpass1
        13.1%
        4.2
        Acute_Fatal_102
        33.0%
        7.2
        24.2%
        10.8
        Acute_Fatal_102._STARpass1
        23.4%
        10.5
        Acute_Fatal_102_1
        84.6%
        53%
        116 bp
        44.8
        Acute_Fatal_102_2
        83.0%
        52%
        115 bp
        44.8
        Acute_Fatal_104
        38.0%
        6.4
        13.5%
        8.5
        Acute_Fatal_104._STARpass1
        13.6%
        8.5
        Acute_Fatal_104_1
        94.1%
        55%
        143 bp
        62.6
        Acute_Fatal_104_2
        92.5%
        55%
        139 bp
        62.6
        Acute_Fatal_105
        40.0%
        2.9
        8.9%
        3.6
        Acute_Fatal_105._STARpass1
        9.0%
        3.7
        Acute_Fatal_105_1
        96.6%
        56%
        144 bp
        40.8
        Acute_Fatal_105_2
        95.5%
        56%
        140 bp
        40.8
        Acute_Fatal_106
        36.8%
        7.2
        20.4%
        9.8
        Acute_Fatal_106._STARpass1
        20.8%
        10.0
        Acute_Fatal_106_1
        91.6%
        55%
        139 bp
        48.2
        Acute_Fatal_106_2
        90.2%
        54%
        136 bp
        48.2
        Acute_Fatal_107
        45.0%
        4.1
        12.9%
        4.5
        Acute_Fatal_107._STARpass1
        12.8%
        4.5
        Acute_Fatal_107_1
        93.8%
        57%
        140 bp
        35.1
        Acute_Fatal_107_2
        92.9%
        56%
        137 bp
        35.1
        Acute_Fatal_109
        15.1%
        0.6
        4.8%
        1.9
        Acute_Fatal_109._STARpass1
        4.9%
        1.9
        Acute_Fatal_109_1
        98.0%
        56%
        144 bp
        39.8
        Acute_Fatal_109_2
        97.2%
        55%
        141 bp
        39.8
        Acute_Fatal_14
        42.8%
        4.0
        12.8%
        4.6
        Acute_Fatal_14._STARpass1
        12.7%
        4.6
        Acute_Fatal_14_1
        90.5%
        55%
        118 bp
        36.1
        Acute_Fatal_14_2
        89.2%
        54%
        117 bp
        36.1
        Acute_Fatal_16
        34.3%
        4.7
        20.3%
        6.9
        Acute_Fatal_16._STARpass1
        20.3%
        6.9
        Acute_Fatal_16_1
        85.6%
        54%
        116 bp
        33.9
        Acute_Fatal_16_2
        83.5%
        53%
        116 bp
        33.9
        Acute_Fatal_17
        33.6%
        2.6
        20.1%
        3.8
        Acute_Fatal_17._STARpass1
        20.0%
        3.8
        Acute_Fatal_17_1
        82.3%
        53%
        116 bp
        18.9
        Acute_Fatal_17_2
        79.7%
        52%
        115 bp
        18.9
        Acute_Fatal_18
        51.1%
        2.4
        8.7%
        2.3
        Acute_Fatal_18._STARpass1
        8.5%
        2.3
        Acute_Fatal_18_1
        90.0%
        57%
        114 bp
        27.0
        Acute_Fatal_18_2
        88.9%
        56%
        112 bp
        27.0
        Acute_Fatal_1_1
        87.9%
        55%
        115 bp
        32.0
        Acute_Fatal_1_2
        87.3%
        54%
        115 bp
        32.0
        Acute_Fatal_20
        39.1%
        2.0
        14.2%
        2.6
        Acute_Fatal_20._STARpass1
        14.3%
        2.6
        Acute_Fatal_20_1
        87.1%
        55%
        115 bp
        18.2
        Acute_Fatal_20_2
        84.7%
        54%
        114 bp
        18.2
        Acute_Fatal_21
        34.6%
        3.2
        18.4%
        4.6
        Acute_Fatal_21._STARpass1
        18.3%
        4.5
        Acute_Fatal_21_1
        84.2%
        54%
        112 bp
        24.7
        Acute_Fatal_21_2
        83.4%
        53%
        111 bp
        24.7
        Acute_Fatal_22
        24.2%
        0.9
        5.6%
        1.9
        Acute_Fatal_22._STARpass1
        5.3%
        1.8
        Acute_Fatal_22_1
        92.1%
        53%
        115 bp
        33.7
        Acute_Fatal_22_2
        91.8%
        53%
        114 bp
        33.7
        Acute_Fatal_24
        27.1%
        2.4
        11.6%
        4.4
        Acute_Fatal_24._STARpass1
        11.8%
        4.5
        Acute_Fatal_24_1
        93.7%
        54%
        112 bp
        38.4
        Acute_Fatal_24_2
        92.9%
        54%
        111 bp
        38.4
        Acute_Fatal_26
        32.3%
        2.0
        19.7%
        3.1
        Acute_Fatal_26._STARpass1
        19.9%
        3.1
        Acute_Fatal_26_1
        90.6%
        52%
        115 bp
        15.8
        Acute_Fatal_26_2
        88.7%
        52%
        114 bp
        15.8
        Acute_Fatal_29
        57.1%
        0.5
        2.2%
        0.4
        Acute_Fatal_29._STARpass1
        2.0%
        0.4
        Acute_Fatal_29_1
        94.2%
        59%
        112 bp
        19.9
        Acute_Fatal_29_2
        94.5%
        58%
        112 bp
        19.9
        Acute_Fatal_32
        36.2%
        4.4
        11.7%
        6.1
        Acute_Fatal_32._STARpass1
        11.4%
        6.0
        Acute_Fatal_32_1
        90.4%
        56%
        115 bp
        52.3
        Acute_Fatal_32_2
        89.7%
        55%
        114 bp
        52.3
        Acute_Fatal_33
        55.7%
        1.9
        7.5%
        1.7
        Acute_Fatal_33._STARpass1
        7.5%
        1.7
        Acute_Fatal_33_1
        91.9%
        57%
        115 bp
        22.6
        Acute_Fatal_33_2
        91.2%
        56%
        114 bp
        22.6
        Acute_Fatal_34
        27.9%
        2.5
        12.4%
        4.4
        Acute_Fatal_34._STARpass1
        12.1%
        4.3
        Acute_Fatal_34_1
        90.2%
        55%
        119 bp
        35.8
        Acute_Fatal_34_2
        89.5%
        54%
        118 bp
        35.8
        Acute_Fatal_35
        20.6%
        2.4
        20.8%
        5.8
        Acute_Fatal_35._STARpass1
        20.8%
        5.8
        Acute_Fatal_35_1
        83.9%
        53%
        119 bp
        27.9
        Acute_Fatal_35_2
        82.4%
        53%
        118 bp
        27.9
        Acute_Fatal_36
        37.7%
        3.3
        15.6%
        4.3
        Acute_Fatal_36._STARpass1
        15.5%
        4.3
        Acute_Fatal_36_1
        87.6%
        54%
        117 bp
        27.9
        Acute_Fatal_36_2
        85.8%
        52%
        117 bp
        27.9
        Acute_Fatal_38
        35.1%
        2.3
        16.4%
        3.3
        Acute_Fatal_38._STARpass1
        16.3%
        3.3
        Acute_Fatal_38_1
        85.0%
        54%
        117 bp
        20.2
        Acute_Fatal_38_2
        84.2%
        53%
        117 bp
        20.2
        Acute_Fatal_39
        32.8%
        2.6
        19.9%
        3.9
        Acute_Fatal_39._STARpass1
        19.8%
        3.9
        Acute_Fatal_39_1
        84.0%
        54%
        116 bp
        19.6
        Acute_Fatal_39_2
        81.6%
        53%
        115 bp
        19.6
        Acute_Fatal_4
        40.1%
        3.2
        16.4%
        4.0
        Acute_Fatal_4._STARpass1
        16.4%
        4.0
        Acute_Fatal_40
        34.9%
        6.5
        19.8%
        9.3
        Acute_Fatal_40._STARpass1
        19.9%
        9.4
        Acute_Fatal_40_1
        87.1%
        54%
        116 bp
        46.9
        Acute_Fatal_40_2
        85.9%
        53%
        116 bp
        46.9
        Acute_Fatal_41
        30.9%
        2.2
        28.0%
        3.5
        Acute_Fatal_41._STARpass1
        28.1%
        3.6
        Acute_Fatal_41_1
        79.1%
        53%
        118 bp
        12.6
        Acute_Fatal_41_2
        76.5%
        52%
        117 bp
        12.6
        Acute_Fatal_42
        34.9%
        4.4
        19.8%
        6.3
        Acute_Fatal_42._STARpass1
        19.8%
        6.3
        Acute_Fatal_42_1
        85.6%
        54%
        118 bp
        31.9
        Acute_Fatal_42_2
        83.4%
        53%
        117 bp
        31.9
        Acute_Fatal_45
        37.7%
        3.1
        18.5%
        4.1
        Acute_Fatal_45._STARpass1
        18.5%
        4.1
        Acute_Fatal_45_1
        86.6%
        54%
        117 bp
        22.1
        Acute_Fatal_45_2
        85.8%
        53%
        117 bp
        22.1
        Acute_Fatal_46
        41.6%
        0.8
        14.8%
        0.9
        Acute_Fatal_46._STARpass1
        14.8%
        0.9
        Acute_Fatal_46_1
        84.6%
        55%
        117 bp
        6.3
        Acute_Fatal_46_2
        82.9%
        54%
        117 bp
        6.3
        Acute_Fatal_47
        39.5%
        1.4
        14.0%
        1.8
        Acute_Fatal_47._STARpass1
        13.9%
        1.8
        Acute_Fatal_47_1
        85.1%
        57%
        117 bp
        12.7
        Acute_Fatal_47_2
        84.1%
        56%
        116 bp
        12.7
        Acute_Fatal_48
        39.4%
        4.2
        15.4%
        5.3
        Acute_Fatal_48._STARpass1
        15.4%
        5.3
        Acute_Fatal_48_1
        86.4%
        55%
        116 bp
        34.3
        Acute_Fatal_48_2
        84.2%
        54%
        115 bp
        34.3
        Acute_Fatal_49
        44.4%
        17.7
        12.8%
        20.0
        Acute_Fatal_49._STARpass1
        12.7%
        19.7
        Acute_Fatal_49_1
        94.0%
        55%
        116 bp
        155.5
        Acute_Fatal_49_2
        93.1%
        54%
        115 bp
        155.5
        Acute_Fatal_4_1
        86.5%
        55%
        117 bp
        24.5
        Acute_Fatal_4_2
        85.5%
        54%
        116 bp
        24.5
        Acute_Fatal_5
        34.2%
        2.5
        24.6%
        3.6
        Acute_Fatal_5._STARpass1
        24.7%
        3.6
        Acute_Fatal_52
        37.0%
        7.7
        21.3%
        10.4
        Acute_Fatal_52._STARpass1
        21.6%
        10.6
        Acute_Fatal_52_1
        88.4%
        53%
        118 bp
        49.0
        Acute_Fatal_52_2
        86.8%
        52%
        117 bp
        49.0
        Acute_Fatal_57
        37.8%
        2.7
        16.7%
        3.6
        Acute_Fatal_57._STARpass1
        16.7%
        3.6
        Acute_Fatal_57_1
        85.6%
        54%
        117 bp
        21.7
        Acute_Fatal_57_2
        83.5%
        53%
        116 bp
        21.7
        Acute_Fatal_58
        40.5%
        2.9
        14.2%
        3.5
        Acute_Fatal_58._STARpass1
        14.0%
        3.5
        Acute_Fatal_58_1
        86.4%
        56%
        114 bp
        25.1
        Acute_Fatal_58_2
        85.8%
        55%
        114 bp
        25.1
        Acute_Fatal_5_1
        79.4%
        53%
        117 bp
        14.6
        Acute_Fatal_5_2
        75.2%
        52%
        115 bp
        14.6
        Acute_Fatal_6
        34.5%
        2.0
        16.8%
        2.9
        Acute_Fatal_6._STARpass1
        16.7%
        2.9
        Acute_Fatal_64
        35.0%
        4.5
        20.7%
        6.5
        Acute_Fatal_64._STARpass1
        20.7%
        6.5
        Acute_Fatal_64_1
        81.6%
        53%
        115 bp
        31.4
        Acute_Fatal_64_2
        80.4%
        52%
        114 bp
        31.4
        Acute_Fatal_65
        56.0%
        0.2
        1.7%
        0.2
        Acute_Fatal_65._STARpass1
        1.6%
        0.1
        Acute_Fatal_65_1
        94.7%
        59%
        115 bp
        9.0
        Acute_Fatal_65_2
        94.5%
        59%
        115 bp
        9.0
        Acute_Fatal_67
        36.4%
        0.5
        16.3%
        0.7
        Acute_Fatal_67._STARpass1
        16.3%
        0.7
        Acute_Fatal_67_1
        81.8%
        52%
        139 bp
        4.0
        Acute_Fatal_67_2
        61.6%
        51%
        123 bp
        4.0
        Acute_Fatal_68
        35.1%
        8.7
        10.5%
        12.4
        Acute_Fatal_68._STARpass1
        10.3%
        12.2
        Acute_Fatal_68_1
        96.0%
        55%
        117 bp
        118.1
        Acute_Fatal_68_2
        94.7%
        54%
        116 bp
        118.1
        Acute_Fatal_69
        34.2%
        2.4
        12.3%
        3.5
        Acute_Fatal_69._STARpass1
        12.4%
        3.5
        Acute_Fatal_69_1
        92.6%
        48%
        118 bp
        28.3
        Acute_Fatal_69_2
        90.7%
        48%
        117 bp
        28.3
        Acute_Fatal_6_1
        84.3%
        54%
        116 bp
        17.5
        Acute_Fatal_6_2
        82.5%
        53%
        115 bp
        17.5
        Acute_Fatal_70
        18.8%
        0.1
        14.4%
        0.3
        Acute_Fatal_70._STARpass1
        14.5%
        0.3
        Acute_Fatal_70_1
        80.5%
        53%
        138 bp
        2.3
        Acute_Fatal_70_2
        56.3%
        52%
        122 bp
        2.3
        Acute_Fatal_71
        18.0%
        0.3
        2.2%
        0.9
        Acute_Fatal_71._STARpass1
        1.3%
        0.5
        Acute_Fatal_71_1
        95.4%
        54%
        119 bp
        40.4
        Acute_Fatal_71_2
        93.8%
        53%
        118 bp
        40.4
        Acute_Fatal_73
        52.7%
        1.3
        3.5%
        1.2
        Acute_Fatal_73._STARpass1
        3.4%
        1.1
        Acute_Fatal_73_1
        96.1%
        57%
        119 bp
        34.0
        Acute_Fatal_73_2
        94.7%
        56%
        119 bp
        34.0
        Acute_Fatal_76
        47.5%
        0.9
        4.7%
        1.0
        Acute_Fatal_76._STARpass1
        4.6%
        0.9
        Acute_Fatal_76_1
        93.7%
        60%
        116 bp
        20.6
        Acute_Fatal_76_2
        93.8%
        60%
        115 bp
        20.6
        Acute_Fatal_86
        49.0%
        2.0
        4.9%
        2.0
        Acute_Fatal_86._STARpass1
        4.8%
        2.0
        Acute_Fatal_86_1
        96.5%
        57%
        121 bp
        41.4
        Acute_Fatal_86_2
        95.0%
        56%
        120 bp
        41.4
        Acute_Fatal_87
        9.0%
        0.7
        27.5%
        4.0
        Acute_Fatal_87._STARpass1
        27.4%
        4.0
        Acute_Fatal_87_1
        81.8%
        52%
        119 bp
        14.6
        Acute_Fatal_87_2
        81.7%
        51%
        118 bp
        14.6
        Acute_Fatal_9
        37.2%
        4.1
        18.2%
        5.6
        Acute_Fatal_9._STARpass1
        18.0%
        5.5
        Acute_Fatal_92
        42.7%
        1.4
        6.1%
        1.7
        Acute_Fatal_92._STARpass1
        5.9%
        1.6
        Acute_Fatal_92_1
        93.0%
        57%
        120 bp
        26.9
        Acute_Fatal_92_2
        92.2%
        56%
        119 bp
        26.9
        Acute_Fatal_93
        32.3%
        2.9
        18.2%
        4.5
        Acute_Fatal_93._STARpass1
        18.4%
        4.5
        Acute_Fatal_93_1
        89.7%
        54%
        121 bp
        24.7
        Acute_Fatal_93_2
        87.7%
        53%
        120 bp
        24.7
        Acute_Fatal_96
        13.9%
        0.1
        1.2%
        0.4
        Acute_Fatal_96._STARpass1
        1.2%
        0.4
        Acute_Fatal_96_1
        91.5%
        50%
        121 bp
        36.0
        Acute_Fatal_96_2
        88.6%
        51%
        121 bp
        36.0
        Acute_Fatal_97
        49.3%
        1.2
        6.5%
        1.2
        Acute_Fatal_97._STARpass1
        6.4%
        1.2
        Acute_Fatal_97_1
        92.9%
        55%
        111 bp
        18.4
        Acute_Fatal_97_2
        91.9%
        54%
        110 bp
        18.4
        Acute_Fatal_99
        58.5%
        1.9
        10.9%
        1.6
        Acute_Fatal_99._STARpass1
        10.8%
        1.6
        Acute_Fatal_99_1
        88.4%
        52%
        110 bp
        14.6
        Acute_Fatal_99_2
        87.9%
        52%
        110 bp
        14.6
        Acute_Fatal_9_1
        88.4%
        54%
        118 bp
        30.6
        Acute_Fatal_9_2
        87.4%
        53%
        117 bp
        30.6
        Acute_Survivor_1
        37.7%
        3.4
        18.7%
        4.5
        Acute_Survivor_1._STARpass1
        18.8%
        4.5
        Acute_Survivor_10
        34.2%
        4.6
        18.9%
        6.7
        Acute_Survivor_10._STARpass1
        18.8%
        6.7
        Acute_Survivor_10_1
        84.5%
        54%
        119 bp
        35.6
        Acute_Survivor_10_2
        83.9%
        52%
        118 bp
        35.6
        Acute_Survivor_11
        30.6%
        4.4
        17.7%
        7.2
        Acute_Survivor_11._STARpass1
        18.1%
        7.3
        Acute_Survivor_11_1
        89.4%
        53%
        115 bp
        40.4
        Acute_Survivor_11_2
        88.1%
        53%
        114 bp
        40.4
        Acute_Survivor_12
        30.2%
        1.3
        21.4%
        2.2
        Acute_Survivor_12._STARpass1
        21.9%
        2.3
        Acute_Survivor_12_1
        84.2%
        53%
        117 bp
        10.3
        Acute_Survivor_12_2
        82.3%
        52%
        116 bp
        10.3
        Acute_Survivor_13
        30.2%
        3.4
        24.8%
        5.6
        Acute_Survivor_13._STARpass1
        25.0%
        5.6
        Acute_Survivor_13_1
        91.2%
        53%
        118 bp
        22.5
        Acute_Survivor_13_2
        87.7%
        52%
        117 bp
        22.5
        Acute_Survivor_14
        41.6%
        6.5
        16.9%
        7.8
        Acute_Survivor_14._STARpass1
        17.0%
        7.9
        Acute_Survivor_14_1
        88.1%
        54%
        116 bp
        46.6
        Acute_Survivor_14_2
        87.1%
        53%
        115 bp
        46.6
        Acute_Survivor_15
        40.4%
        6.4
        15.8%
        8.0
        Acute_Survivor_15._STARpass1
        15.3%
        7.7
        Acute_Survivor_15_1
        86.2%
        54%
        110 bp
        50.5
        Acute_Survivor_15_2
        87.2%
        54%
        109 bp
        50.5
        Acute_Survivor_16
        40.6%
        6.9
        20.3%
        8.5
        Acute_Survivor_16._STARpass1
        20.3%
        8.4
        Acute_Survivor_16_1
        84.8%
        54%
        117 bp
        41.6
        Acute_Survivor_16_2
        84.0%
        53%
        116 bp
        41.6
        Acute_Survivor_17
        37.9%
        3.2
        18.9%
        4.2
        Acute_Survivor_17._STARpass1
        18.7%
        4.1
        Acute_Survivor_17_1
        83.9%
        54%
        116 bp
        22.1
        Acute_Survivor_17_2
        82.4%
        53%
        115 bp
        22.1
        Acute_Survivor_18
        35.2%
        5.5
        20.4%
        7.8
        Acute_Survivor_18._STARpass1
        20.3%
        7.7
        Acute_Survivor_18_1
        82.0%
        54%
        117 bp
        38.1
        Acute_Survivor_18_2
        81.0%
        53%
        116 bp
        38.1
        Acute_Survivor_19
        37.4%
        0.3
        5.7%
        0.4
        Acute_Survivor_19._STARpass1
        5.7%
        0.4
        Acute_Survivor_19_1
        92.7%
        55%
        120 bp
        6.9
        Acute_Survivor_19_2
        90.1%
        55%
        118 bp
        6.9
        Acute_Survivor_1_1
        87.0%
        54%
        119 bp
        24.0
        Acute_Survivor_1_2
        85.0%
        53%
        118 bp
        24.0
        Acute_Survivor_2
        32.9%
        3.0
        17.3%
        4.5
        Acute_Survivor_2._STARpass1
        17.3%
        4.5
        Acute_Survivor_20
        33.5%
        2.1
        23.1%
        3.2
        Acute_Survivor_20._STARpass1
        23.3%
        3.2
        Acute_Survivor_20_1
        89.2%
        53%
        120 bp
        13.8
        Acute_Survivor_20_2
        87.3%
        52%
        119 bp
        13.8
        Acute_Survivor_21
        56.7%
        1.4
        5.6%
        1.3
        Acute_Survivor_21._STARpass1
        5.4%
        1.2
        Acute_Survivor_21_1
        94.1%
        57%
        119 bp
        22.6
        Acute_Survivor_21_2
        93.1%
        56%
        119 bp
        22.6
        Acute_Survivor_22
        32.9%
        2.5
        20.1%
        3.8
        Acute_Survivor_22._STARpass1
        20.8%
        3.9
        Acute_Survivor_22_1
        88.1%
        54%
        118 bp
        18.8
        Acute_Survivor_22_2
        86.6%
        53%
        117 bp
        18.8
        Acute_Survivor_23
        24.4%
        0.1
        22.9%
        0.1
        Acute_Survivor_23._STARpass1
        23.0%
        0.1
        Acute_Survivor_23_1
        78.2%
        52%
        121 bp
        0.6
        Acute_Survivor_23_2
        72.1%
        51%
        120 bp
        0.6
        Acute_Survivor_24
        32.2%
        3.0
        14.6%
        4.6
        Acute_Survivor_24._STARpass1
        14.4%
        4.6
        Acute_Survivor_24_1
        92.4%
        55%
        118 bp
        31.9
        Acute_Survivor_24_2
        91.5%
        54%
        117 bp
        31.9
        Acute_Survivor_25
        33.5%
        0.5
        16.8%
        0.8
        Acute_Survivor_25._STARpass1
        16.7%
        0.8
        Acute_Survivor_25_1
        86.0%
        54%
        121 bp
        4.8
        Acute_Survivor_25_2
        81.0%
        53%
        120 bp
        4.8
        Acute_Survivor_26
        5.9%
        0.2
        33.6%
        1.4
        Acute_Survivor_26._STARpass1
        34.7%
        1.4
        Acute_Survivor_26_1
        88.2%
        51%
        120 bp
        4.1
        Acute_Survivor_26_2
        84.6%
        50%
        119 bp
        4.1
        Acute_Survivor_27
        7.8%
        1.7
        47.7%
        11.1
        Acute_Survivor_27._STARpass1
        47.7%
        11.1
        Acute_Survivor_27_1
        86.9%
        47%
        116 bp
        23.3
        Acute_Survivor_27_2
        84.8%
        47%
        116 bp
        23.3
        Acute_Survivor_28
        45.0%
        10.7
        9.4%
        11.9
        Acute_Survivor_28._STARpass1
        9.3%
        11.8
        Acute_Survivor_28_1
        95.5%
        56%
        120 bp
        127.1
        Acute_Survivor_28_2
        94.4%
        55%
        119 bp
        127.1
        Acute_Survivor_29
        29.2%
        0.6
        10.2%
        1.0
        Acute_Survivor_29._STARpass1
        10.2%
        1.0
        Acute_Survivor_29_1
        91.7%
        55%
        120 bp
        10.0
        Acute_Survivor_29_2
        91.0%
        54%
        120 bp
        10.0
        Acute_Survivor_2_1
        85.3%
        54%
        117 bp
        26.2
        Acute_Survivor_2_2
        83.8%
        53%
        116 bp
        26.2
        Acute_Survivor_3
        36.7%
        0.1
        13.2%
        0.1
        Acute_Survivor_3._STARpass1
        13.2%
        0.1
        Acute_Survivor_30
        49.6%
        1.6
        5.5%
        1.6
        Acute_Survivor_30._STARpass1
        5.3%
        1.5
        Acute_Survivor_30_1
        94.2%
        57%
        120 bp
        28.5
        Acute_Survivor_30_2
        93.6%
        56%
        119 bp
        28.5
        Acute_Survivor_31
        52.5%
        4.6
        9.2%
        4.3
        Acute_Survivor_31._STARpass1
        9.1%
        4.3
        Acute_Survivor_31_1
        94.2%
        55%
        117 bp
        47.2
        Acute_Survivor_31_2
        92.8%
        54%
        116 bp
        47.2
        Acute_Survivor_32
        24.9%
        0.0
        6.4%
        0.1
        Acute_Survivor_32._STARpass1
        6.3%
        0.1
        Acute_Survivor_32_1
        65.7%
        55%
        124 bp
        1.1
        Acute_Survivor_32_2
        44.7%
        54%
        115 bp
        1.1
        Acute_Survivor_33
        18.3%
        0.2
        8.0%
        0.7
        Acute_Survivor_33._STARpass1
        7.9%
        0.7
        Acute_Survivor_33_1
        88.6%
        52%
        92 bp
        8.3
        Acute_Survivor_33_2
        88.0%
        51%
        92 bp
        8.3
        Acute_Survivor_34
        33.1%
        0.1
        9.4%
        0.2
        Acute_Survivor_34._STARpass1
        9.3%
        0.2
        Acute_Survivor_34_1
        72.4%
        52%
        99 bp
        1.7
        Acute_Survivor_34_2
        71.8%
        52%
        99 bp
        1.7
        Acute_Survivor_35
        18.7%
        0.1
        24.1%
        0.3
        Acute_Survivor_35._STARpass1
        24.4%
        0.3
        Acute_Survivor_35_1
        83.7%
        51%
        115 bp
        1.2
        Acute_Survivor_35_2
        80.7%
        50%
        114 bp
        1.2
        Acute_Survivor_36
        44.2%
        1.9
        11.7%
        2.1
        Acute_Survivor_36._STARpass1
        11.8%
        2.1
        Acute_Survivor_36_1
        91.5%
        57%
        139 bp
        18.2
        Acute_Survivor_36_2
        90.6%
        57%
        136 bp
        18.2
        Acute_Survivor_37
        36.4%
        8.4
        19.2%
        11.5
        Acute_Survivor_37._STARpass1
        19.2%
        11.5
        Acute_Survivor_37_1
        92.5%
        55%
        142 bp
        59.9
        Acute_Survivor_37_2
        91.1%
        54%
        139 bp
        59.9
        Acute_Survivor_38
        31.3%
        3.0
        15.3%
        4.8
        Acute_Survivor_38._STARpass1
        15.6%
        4.8
        Acute_Survivor_38_1
        93.6%
        55%
        141 bp
        31.1
        Acute_Survivor_38_2
        92.3%
        54%
        137 bp
        31.1
        Acute_Survivor_39
        59.1%
        4.6
        8.4%
        3.9
        Acute_Survivor_39._STARpass1
        8.4%
        3.9
        Acute_Survivor_39_1
        95.5%
        57%
        141 bp
        46.2
        Acute_Survivor_39_2
        94.4%
        56%
        138 bp
        46.2
        Acute_Survivor_3_1
        71.0%
        55%
        135 bp
        0.8
        Acute_Survivor_3_2
        51.2%
        53%
        120 bp
        0.8
        Acute_Survivor_4
        32.8%
        1.6
        20.4%
        2.5
        Acute_Survivor_4._STARpass1
        20.4%
        2.5
        Acute_Survivor_40
        40.7%
        8.1
        21.0%
        10.0
        Acute_Survivor_40._STARpass1
        21.3%
        10.1
        Acute_Survivor_40_1
        89.5%
        55%
        141 bp
        47.5
        Acute_Survivor_40_2
        87.9%
        54%
        137 bp
        47.5
        Acute_Survivor_41
        33.4%
        5.2
        17.9%
        7.7
        Acute_Survivor_41._STARpass1
        18.5%
        8.0
        Acute_Survivor_41_1
        92.8%
        55%
        141 bp
        43.3
        Acute_Survivor_41_2
        91.4%
        55%
        138 bp
        43.3
        Acute_Survivor_42
        37.8%
        3.6
        16.6%
        4.8
        Acute_Survivor_42._STARpass1
        16.6%
        4.8
        Acute_Survivor_42_1
        91.5%
        55%
        141 bp
        28.7
        Acute_Survivor_42_2
        90.1%
        55%
        138 bp
        28.7
        Acute_Survivor_43
        37.1%
        6.9
        21.7%
        9.3
        Acute_Survivor_43._STARpass1
        21.8%
        9.4
        Acute_Survivor_43_1
        89.3%
        54%
        140 bp
        43.0
        Acute_Survivor_43_2
        87.5%
        53%
        137 bp
        43.0
        Acute_Survivor_44
        42.8%
        4.0
        13.8%
        4.7
        Acute_Survivor_44._STARpass1
        13.9%
        4.8
        Acute_Survivor_44_1
        92.2%
        57%
        141 bp
        34.1
        Acute_Survivor_44_2
        91.3%
        56%
        138 bp
        34.1
        Acute_Survivor_45
        34.1%
        8.1
        19.7%
        12.0
        Acute_Survivor_45._STARpass1
        19.7%
        11.9
        Acute_Survivor_45_1
        92.5%
        55%
        144 bp
        60.6
        Acute_Survivor_45_2
        91.0%
        54%
        141 bp
        60.6
        Acute_Survivor_4_1
        82.8%
        54%
        118 bp
        12.0
        Acute_Survivor_4_2
        80.9%
        52%
        118 bp
        12.0
        Acute_Survivor_5
        45.5%
        4.1
        13.7%
        4.5
        Acute_Survivor_5._STARpass1
        13.7%
        4.5
        Acute_Survivor_5_1
        86.5%
        54%
        112 bp
        32.5
        Acute_Survivor_5_2
        85.2%
        54%
        112 bp
        32.5
        Acute_Survivor_6
        50.5%
        1.5
        6.5%
        1.5
        Acute_Survivor_6._STARpass1
        6.4%
        1.5
        Acute_Survivor_6_1
        93.0%
        56%
        116 bp
        23.2
        Acute_Survivor_6_2
        92.5%
        56%
        115 bp
        23.2
        Acute_Survivor_7
        45.2%
        1.8
        14.7%
        2.0
        Acute_Survivor_7._STARpass1
        14.8%
        2.0
        Acute_Survivor_7_1
        88.5%
        55%
        119 bp
        13.6
        Acute_Survivor_7_2
        87.9%
        54%
        118 bp
        13.6
        Acute_Survivor_8
        26.6%
        0.1
        6.0%
        0.1
        Acute_Survivor_8._STARpass1
        5.9%
        0.1
        Acute_Survivor_8_1
        86.3%
        51%
        120 bp
        1.8
        Acute_Survivor_8_2
        82.8%
        51%
        119 bp
        1.8
        Acute_Survivor_9
        2.1%
        0.2
        11.4%
        4.7
        Acute_Survivor_9._STARpass1
        11.4%
        4.7
        Acute_Survivor_9_1
        89.7%
        47%
        118 bp
        41.4
        Acute_Survivor_9_2
        86.5%
        46%
        117 bp
        41.4

        featureCounts

        Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

        loading..

        STAR

        STAR is an ultrafast universal RNA-seq aligner.

        Alignment Scores

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        loading..

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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